Set up payroll

Before you can pay anyone, Bokapsys needs to know who your business is to the tax authorities, which pay items to calculate, how often you pay, and which states you are registered in. This page walks through each part of setup, in the order that avoids rework, and explains every field.

Setup is spread over a few pages because it touches both Payroll and Tax. The Get started with Payroll checklist on the Payroll Dashboard keeps track of what is done and sends you to the right place for each step. See Payroll overview for what each checklist step means.

1. 1Company tax details
2. 2Pay schedule
3. 3Standard pay items
4. 4Employees
5. 5Federal registration
6. 6State registrations
7. 7Deposit schedule

Before you start

You need a role that can change payroll and tax settings (by default Super admin, Admin or CFO). Payroll and Tax are included in every workspace; if either group is missing from your sidebar, see Payroll overview.

Gather these first:

What	Where to find it
Your EIN (Employer Identification Number), 9 digits	IRS letter CP 575 (the letter confirming your EIN), or the top of any Form 941 or W-2 you have filed.
Your legal business name and address	The same IRS letter. Use the name exactly as the IRS has it.
Your state withholding account number for each state	The state’s registration letter, or the state’s online account.
Your state unemployment (SUI) rate and taxable wage base for each state	The rate notice your state unemployment agency sends you each year (often in December). New employers get a “new employer rate” in their registration letter.
How often each state wants withholding paid, and on which day	The same state withholding registration letter, or the state’s online account.
Whether you are a monthly or semi-weekly federal depositor	The IRS notice you receive each year (usually in November). New employers are normally monthly depositors.
Optional: your SSA Business Services Online (BSO) user ID and your IRS TCC	Your Social Security BSO account, and the Transmitter Control Code the IRS gave you for its 1099 filing site (IRIS). Only needed at year end.

Step 1: Enter your company’s tax details

Your company’s tax record is called a taxpayer in Bokapsys. It holds the EIN that goes on your 941s, W-2s and 1099s.

1. In the sidebar, open Tax → Tax Setup. The Taxpayers tab opens.
2. Click Add taxpayer. The Add taxpayer window opens.
3. Fill in the fields described in the table below.
4. Tick This is the entity that files your returns if this is your main business (it usually is).
5. Click Save. You see the message Taxpayer added, and the taxpayer appears in the list with only the last four digits of the EIN showing.

Field	Required	What it means	Example
Legal name	Yes	Your business’s legal name, exactly as on your IRS letter.	Maple Street Bakery LLC
Trading name (optional)	No	A shorter name used on screen.	Maple Street Bakery
Entity kind	No	Business, Individual, Trust, Estate, Non-profit or Government.	Business
Business structure	No	For a business: how it is set up for income tax, such as Single-member LLC or S corporation.	Single-member LLC
Tax ID type	No	The kind of tax number. Choose EIN (Employer Identification Number) for an employer.	EIN
Employer Identification Number	Needed for year-end files	Your 9-digit EIN. You can type it with or without the hyphen. It is stored encrypted and only the last four digits are ever shown.	12-3456789
Street address, Address line 2, City, State, ZIP code	No, but recommended	Your business address as the IRS has it.	120 Maple St, Columbus, Ohio, 43215
State employer account number	No	From your state unemployment registration. It goes on the W-2.	1234567
Social Security BSO user ID	Only for filing W-2s yourself	Your user ID on the SSA’s Business Services Online site.	ABCD1234
Employer signature PIN	Only for filing W-2s yourself	The PIN shown in Business Services Online. It signs your W-2 file. Stored encrypted.
Kind of employer, Employment type	Only for filing W-2s yourself	How the SSA classifies your business; most private businesses keep the defaults.
IRS 1099 code (TCC)	Only for filing 1099s yourself	The 5-character code the IRS gave you for its 1099 site.	A1B2C
Contact name, Contact phone, Contact email	No	The person the agencies should contact about your filings.	Jane Park, 614-555-0100, jane@example.com

How to check it worked: on the Payroll Dashboard, Enter your employer tax number is ticked.

Common problems

Message	What it means and how to fix it
Enter the legal name exactly as the IRS has it.	Fill in Legal name.
A tax ID has nine digits.	The EIN must have exactly 9 digits. Check the IRS letter.
The step stays unticked	The EIN was left blank, or only its last four digits are on file. Click the pencil next to the taxpayer and enter the full number. When editing, the box shows “On file, ending 6789” if the full number is already saved.

To change details later, click the pencil icon on the taxpayer’s row.

Your payslips print the legal name, address and Contact phone of this primary taxpayer. If no taxpayer is set up yet, or the phone is blank, they use what is in Company settings instead. See Company settings.

Step 2: Create a pay schedule

A pay schedule says how often you pay people: weekly, every two weeks, twice a month or monthly. Go to Payroll → Payroll Settings, stay on the Pay Schedules tab and click New schedule. Pay schedules explains every field.

Step 3: Add the standard US pay items

Pay items are the lines on a payslip: salary, overtime, each tax. Instead of building them yourself, you add the standard US set in one click.

1. Open Payroll → Compensation. The Pay Components list opens.
2. Click Set up US payroll.
3. You see US payroll set up with a line such as “14 standard pay items added”. The list now shows the standard items, each marked Standard.

Setup adds these fourteen items:

Item	Type	What it is
Salary	Earning	For salaried employees: the annual salary divided by the number of pay periods in a year.
Regular Pay	Earning	For hourly employees: hours worked × hourly rate.
Overtime	Earning	Overtime hours × hourly rate × 1.5.
Double Time	Earning	Double-time hours × hourly rate × 2.
Paid Time Off	Earning	Vacation, sick, holiday and other paid time-off hours × hourly rate.
Federal Withholding	Employee tax	Federal income tax, worked out from the employee’s W-4 using the IRS method.
Social Security	Employee tax	The employee’s share of Social Security.
Medicare	Employee tax	The employee’s share of Medicare, plus the Additional Medicare Tax on high earners.
State Withholding	Employee tax	State income tax for the employee’s state.
Local Withholding	Employee tax	City, county or school-district tax you entered for the employee.
Social Security (Employer)	Employer tax	Your matching share of Social Security. Not shown on the payslip.
Medicare (Employer)	Employer tax	Your matching share of Medicare. Not shown on the payslip.
FUTA	Employer tax	Federal unemployment tax. Not shown on the payslip.
State Unemployment (Employer)	Employer tax	State unemployment tax from your registration’s rate. Not shown on the payslip.

The items start on 1 January of the current year, even if you click the button in October. That way Bokapsys can calculate any earlier pay periods of this year correctly. Clicking Set up US payroll again is safe: it adds anything missing and brings existing standard items up to date (including moving their start date back to 1 January if needed). It never creates duplicates. If everything is already in place you see US payroll is already set up.

For 2026, the figures built into these items include a 6.2% Social Security rate on wages up to $184,500 per employee, a 1.45% Medicare rate (plus 0.9% Additional Medicare Tax for the employee only, on wages above $200,000), and FUTA at 0.6% on the first $7,000 of each employee’s wages. These are the 2026 figures in the app.

How to check it worked: on the Payroll Dashboard, Set up pay items is ticked.

Step 4: Add your employees

Go to Payroll → People → Employees and click Add employee. Employees explains every field, including the W-4. Give every employee a Work state, or no state tax is worked out for them. If you are moving from another provider, you can import your employees from a file instead; see Switching providers.

Step 5: Register for federal payroll tax

Telling Bokapsys you are registered with the IRS for payroll is what creates your federal deposit dates and your Form 941, Form 940, W-2 and 1099 filings in the tax calendar.

1. Open Tax → Tax Setup and click the Jurisdictions tab.
2. At the top, in the registrations section, click Register jurisdiction. The Add a registration window opens.
3. In Where you are registered, choose the federal option (marked Federal).
4. In Registered for, choose Payroll withholding.
5. In How often you file, choose Quarterly (the Form 941 is filed quarterly).
6. Leave the other fields blank and click Register. You see Registration added.

How to check it worked: on the Payroll Dashboard, Register for federal payroll tax is ticked.

Step 6: Register in each state where you employ people

Register every state that appears as a Work state on any of your employees. A state is ticked off as soon as it has any registration, but most states need two: one for withholding (state income tax) and one for unemployment (SUI). States with no income tax, such as Texas or Florida, need only the unemployment registration.

Register for state withholding

1. On Tax → Tax Setup → Jurisdictions, click Register jurisdiction.
2. In Where you are registered, choose the state, for example Ohio.
3. In Registered for, choose Payroll withholding.
4. Fill in the fields below and click Register.

Field	Required	What it means	Example
How often you file	Yes (has a default)	How often you file the state’s withholding return: Monthly, Quarterly or Annually. From your state registration letter.	Quarterly
Account number, last 4 digits	No	The last four digits of your state withholding account number, so you can recognise it.	4821
Full state account number	Recommended	Printed on your state registration notice. It goes in box 15 of each W-2, and is stored encrypted.	1234-5678
How often the state wants withholding paid	No, but recommended	Your state deposit schedule: Next day, Semi-weekly, Weekly, Eighth-monthly, Twice a month, Monthly, Quarterly or Annually. From the same letter. Leave it on Not set if you don’t know.	Monthly
Day of the month it is due	No, but recommended	The day after each period ends when the payment is due, for example 15 for “the 15th of the following month”.	15
State website you sign in to	No	The https address of the state website where you file and pay. Bokapsys links to it from each filing.	https://example.state.gov/business

Bokapsys never makes up a state deposit date. If you leave Day of the month it is due blank, the deposits page shows the period and the amount withheld but no due date, with a note saying why. See Deposits.

Register for state unemployment (SUI)

1. Click Register jurisdiction again.
2. Choose the same state in Where you are registered.
3. In Registered for, choose State unemployment (SUI). Two more fields appear.
4. Fill in the fields below and click Register. A line under the fields shows the most unemployment tax that rate and wage base can charge per employee per year, so you can sanity-check what you typed.

Field	Required	What it means	Example
How often you file	Yes (has a default)	How often you file the state’s unemployment wage report. Usually quarterly.	Quarterly
Account number, last 4 digits	No	Last four digits of your state unemployment account number.	7730
Your unemployment tax rate (%)	Yes, for tax to be charged	Your unemployment tax rate as a percentage, from this year’s rate notice. Type 2.7 for 2.7%.	2.7
Taxable wage base per employee	Yes, for tax to be charged	The amount of each employee’s wages per calendar year that the state taxes, in dollars, from the same notice. Once an employee has earned this much in the year, no more unemployment tax is charged on them.	9000
State website you sign in to	No	The state website where you file.	https://example.state.gov/uitax

Every state sets its own rate and wage base, and both usually change each year. Bokapsys does not guess your rate or your wage base. Without both, unemployment tax for that state is charged as zero, the dashboard step Enter your unemployment rate and wage base stays red, and each pay run shows a warning. If you type a rate below 0.1, the checklist flags it, because it usually means a fraction (0.027) was typed instead of a percentage (2.7).

Changing a registration

To change a rate, wage base or due day, click the pencil icon on the registration’s row in the registrations list. The Edit … registration window opens with the current values; the place and what it is registered for can’t be changed. Change what you need and click Save. You see Registration updated.

When your new SUI rate notice arrives each year, update the rate and wage base this way before the first payroll of the year.

How to check it worked: on the Payroll Dashboard, Register in each state you employ people and Enter your unemployment rate and wage base are both ticked. The registrations list on the Jurisdictions tab shows each one.

Build your tax calendar

Once your registrations are in, click Rebuild calendar next to Register jurisdiction. Bokapsys builds your filing and payment due dates for the year. See Tax calendar.

Step 7: Confirm your federal deposit schedule

A deposit is a payment of the payroll taxes you have withheld and owe. The IRS puts every employer on one of two schedules:

• Monthly: you pay each month’s tax by the 15th of the following month.
• Semi-weekly: you pay within a few banking days of each payday.

The IRS decides which one applies from your lookback period (the 12 months from 1 July two years ago to 30 June last year), and tells you in a notice. Bokapsys can work it out from the payroll it holds, but if you joined part way through the lookback period it cannot see all of it, so you should tell it what the IRS said.

1. Open Tax → Deposits Due.
2. At the top you see a card such as You are a monthly depositor, with the reason, the lookback period and the tax Bokapsys found in it.
3. Click Set what the IRS told you. The Your federal deposit schedule window opens.
4. In Deposit schedule, choose Monthly or Semi-weekly, as your IRS notice says.
5. If you ran payroll with another provider during the lookback period, enter in Tax reported in the lookback period the total tax reported on those Forms 941, in dollars, for example 12345.67. Otherwise leave it blank.
6. Tick This business is enrolled in EFTPS if it is.
7. Click Save. The card now shows a You set this badge.

If you leave Deposit schedule on Work it out from my payroll, Bokapsys keeps estimating from your payroll. A yellow note Bokapsys cannot see the whole lookback period warns you when that estimate is incomplete.

How to check it worked: on the Payroll Dashboard, Confirm your federal deposit schedule is ticked. Deposits explains the deposit dates in full.

Step 8: Switching from another provider mid-year

If you have already paid people this calendar year through another payroll provider, Bokapsys needs each person’s year-to-date totals. Without them, annual limits such as the Social Security wage limit and the FUTA and SUI wage bases start again from zero, and too much tax is taken. Import them under Payroll → Payroll Settings → Import from previous provider. See Switching providers.

If this is your first payroll of the year, skip this step.

How to check setup is complete

Open Payroll → Payroll Dashboard. Every step in Get started with Payroll should be ticked or clearly not apply to you, with no red lines. Then create a pay run and calculate it (see Run payroll). If the amber card Some tax could not be worked out appears, it names the employee and state and tells you what is missing.

Warning on a pay run	What to do
“No state unemployment tax was calculated for US-OH - register for US-OH unemployment tax and enter your rate in Tax Setup” (or “add the US-OH taxable wage base to that registration”)	Complete the SUI registration in Step 6.
Bokapsys does not yet hold a state’s withholding tables	Enter a figure for that employee. See Withholding and State coverage.
A state’s figures have not been checked against the state’s own current publication	Compare the amount with your state’s tables, and enter a figure for the employee if it differs. See Withholding.
Reciprocity agreement but no exemption certificate on file	Tax was withheld for the work state. See Withholding.

Related

Payroll overview

Pay schedules

Employees

Tax setup

Deposits

Run payroll